# mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees

## Documentation for package ‘kinship’ version 1.1.0-23

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

%*% | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%-method | Class "bdsmatrix"
%*%-method | Class "gchol.bdsmatrix"
%*%-method | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%-methods | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%.default | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
%*%.gchol.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
align.pedigree | Generate plotting information for a pedigree
alignped1 | Generate plotting information for a pedigree
alignped2 | Generate plotting information for a pedigree
alignped3 | Generate plotting information for a pedigree
alignped4 | Generate plotting information for a pedigree
all-method | Class "bdsmatrix"
any-method | Class "bdsmatrix"
as.matrix.bdsmatrix | a function for bdsmatrix
as.matrix.gchol | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
as.matrix.gchol.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
as.vector.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
autohint | Align a pedigree to print well
bdsBlock | Block diagonal matrices.
bdsI | Sparse identity matrices
bdsmatrix | Create a sparse symmetric block diagonal matrix object
bdsmatrix-class | Class "bdsmatrix"
bdsmatrix.ibd | Create a bdsmatrix from a list
bdsmatrix.reconcile | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
besthint | Create a hints matrix for a pedigree.
coerce-method | Class "bdsmatrix"
coerce-method | Class "gchol"
coerce-method | Class "gchol.bdsmatrix"
coxme | Fit a mixed-effects Cox model
coxme.control | Control parameters for coxme
coxme.fit | Fit a mixed-effects Cox model
coxme.varcheck | Fit a mixed-effects Cox model
diag-method | Class "bdsmatrix"
diag-method | Class "gchol"
diag-method | Class "gchol.bdsmatrix"
diag<--method | Class "bdsmatrix"
dim-method | Class "bdsmatrix"
dim-method | Class "gchol.bdsmatrix"
dimnames-method | Class "bdsmatrix"
dimnames<--method | Class "bdsmatrix"
familycheck | Error check for a family classification
gchol | Generalized Cholesky decompostion
gchol-class | Class "gchol"
gchol-method | Methods for Function gchol in Package 'kinship'
gchol-methods | Methods for Function gchol in Package 'kinship'
gchol.bdsmatrix | Generalized Cholesky decompostion
gchol.bdsmatrix-class | Class "gchol.bdsmatrix"
getCovariateFormula2 | Linear Mixed Effects model using a kinship matrix.
getCrossedTerms | Linear Mixed Effects model using a kinship matrix.
getGroupsFormula2 | Linear Mixed Effects model using a kinship matrix.
is.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.gchol.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.list.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.list.gchol.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.matrix.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
is.matrix.gchol.bdsmatrix | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix
kindepth | Compute a kinship matrix
kinship | Compute a kinship matrix
list or NULL-class | Class "list or NULL"
lmekin | Linear Mixed Effects model using a kinship matrix.
makefamid | Identify family groups
makekinship | Create a sparse kinship matrix
Math-method | Class "bdsmatrix"
Math2-method | Class "bdsmatrix"
max-method | Class "bdsmatrix"
min-method | Class "bdsmatrix"
Ops-method | Class "bdsmatrix"
pedigree | Create pedigree structure
plot.pedigree | plot pedigrees
print.bdsmatrix | Create a sparse symmetric block diagonal matrix object
print.coxme | Fit a mixed-effects Cox model
print.lmekin | Linear Mixed Effects model using a kinship matrix.
prod-method | Class "bdsmatrix"
range-method | Class "bdsmatrix"
show-method | Class "bdsmatrix"
show-method | Class "gchol"
show-method | Class "gchol.bdsmatrix"
solve.bdsmatrix | Solve a matrix equation using the generalized Cholesky decompostion
solve.gchol | Solve a matrix equation using the generalized Cholesky decompostion
solve.gchol.bdsmatrix | function solve for gchol.bdsmatrix
strata2 | Control parameters for coxme
sum-method | Class "bdsmatrix"
unique-method | Class "bdsmatrix"
[-method | Class "bdsmatrix"
[-method | Class "gchol.bdsmatrix"
[.pedigree | Basic Linear Algebra for classes bdsmatrix and gchol.bdsmatrix